SAM-236 - simplify testing, part 1

The seed of this set of changes is to replace the usage of sed with Python's jinja2to create the testing configuration file.

Using sed is problematic for at least the following reasons:

although commonly found by default on all unix-like systems such as Ubuntu Linux and macOS, it is not the same across all such platforms,
It's usage for rendering a template is atypical at KBase and relies upon an idiosyncratic usage, and
it requires one line (invocation of sed) per substitution

On the other hand, jinja2 is:

widely used at KBase,
is well documented and uses a uniform template format,
requires just one call per template render (no matter the number of substitutions), and
is already a dependency of this project.

This change was originally part of branch feature-SAM-232, but was extracted in order to allow that set of changes to be smaller.

While implementing this change alone, additional issues required resolution:

There is no direct support for local testing
- for instance, the sed template processing is only to be found in the GHA Workflow
- added a script for test preparation which performs OS detection and supports macos and linux
- test preparation and test running entrypoints the same for GHA and local testing.
pipenv development dependencies are not pinned, and many dependencies are quite out of date
- this makes adding or modifying any dependency difficult, especially since pipenv is not always very helpful when tracking down such issues
- Mypy tests were not passing, requiring a dependency update to resolve, thus forcing the issue
coverage reporting is lacking
- not separately reported in GHA workflow
- no generation of html for local testing usage
- no generation of lcov for usage by codecov

Summary of Changes

Replace usage of sed for test config generation to a script render-template.py which wraps jinja2
rename test.cfg.example to test.cfg.template to signify this change
Extract test preparation from GHA workflow non_sdk_test.yml into test/scripts/test-setup.sh, which can be invoked with make test-setup and installs all test service binaries into a common location (test/bin)
make test works again, but not for kb-sdk tests, rather it performs test setup and test running.
ignore more files, especially local development and testing artifacts
update Python dependencies
update testing docs
minor fixes:
- type hint required for mongo_controller.py